- v358 Preview 1 - 6 Nov 2017
- v358 Preview 2 - 13 Nov 2017
- v358 Final - 27 Nov 2017
Code changes:
- Added support for bigNarrowPeak in hubs and custom tracks (#18726). Brian
- Extend trackDb pennantIcon setting to support arbitrary text (e.g. for 'New' tag) (#20270). Kate
- Show schema for bigDataUrl tracks on hgc and hgTrackUi (#20281). Brian
- Turn on 50 million line limit for loading bed files as custom tracks (#20541). Hiram
- Add source code version printout to most kent commands does not work on the older code. Hiram
- Add database to Genome Browser page title (appears in browser tab). Kate
- Replace en-dash and em-dash with hyphen in input in hgGateway and hgTracks. Brian
- Fixed problem where disconnect hub button disconnected the wrong hub (#19427). Brian
- Fixed problem with sessions to a file after forms based cartDump (#19914). Brian
- Changed error message for missing id in refLink (#20505). Brian
- Changed the order of loading hubs and copying custom tracks in session loads. Brian
- Change to not check for table presence for bigBed searchType because bigBed tracks may not have a table. Brian
- Minor bugfixes: Angie
- Changes to allow automatically configuring GBiC installed mirrors to download from hgdownload-euro, and text to mention CyVerse on hgCustom and hgHubConnect (#12822). Christopher
- Fixed bug where transMapPslToGenePred did not set the cdsStartStat/cdsEndStat correctly. Mark
- Changes to doNcbiRefSeq.pl: if NCBI doesn't provide RNA sequence for mitochondrial genes then extract it from genomic sequence (#18997). Angie
- Changes to tdbQuery: don't skip databases that don't have own trackDb.ra. Angie
- Changes to printDataVersion: prefer trackDb dataVersion setting to hgFixed.trackVersion (#18997). Angie
- Improving cdwWebBrowse's pie charts by adding an "other" slice that lumps together small slices used in CIRM. Jim
- Third major version of metadata schemas and examples for HCA making v3. Jim
- Making tagStorm more flexible about handling arrays and objects, largely by allowing dots as well as underbars in field names, and such constructs as sample.donor.1.species, sample.donor.1.age, sample.donor.2.species, sample.donor.2.age, to handle arrays of objects. Jim
- Changed cdw in order to save space, it now uses symlinks instead of copying. Galt
- Added a new utility to find symlinkable files for cdw. Galt
- Changed cdwUnlockSubmittedFile.csh to allow wranglers to change a submitted file from a symlink in the submit/ dir back to an file that can be edited again. Galt
- Enhanced cdwsubmyt to now detect a bad path early (one that is already a symlink to the /data/cirm/cdw/) so there is no need to clean up a half-finished submit. Galt
- Added new single_cell tag to cdw. Added definitions for csv support. Galt
- Updates to CIRM download tool and the LOVD browser track. Max
Data changes:
- 30-way multiple alignment on hg38 (27 primates) QA ready (#20216). Hiram
- Added dataVersion /gbdb/$D/ncbiRefSeq/ncbiRefSeqVersion.txt for ncbiRefSeq* (#18997). Angie
- Updated the GWAS and OMIM automated track pipelines to use dbSNP build 150 for variant associations (#18151). Jonathan
- Reset chainNet composite tracks for hg19 and hg38 for better organization (#20216). Hiram
- Added lastz chainNet gorGor5 to hg19 per user request (#20482). Hiram
- Improvements to hgFind search spec for ncbiRefSeq* tracks. Angie